|
| Status |
Public on Oct 01, 2020 |
| Title |
Abraxane_4 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: MDA-MB-231
host mouse strain: balb/c nude
tissue: mammary gland
|
| Treatment protocol |
MDA-MB-231 Cells 2 x 10^6 in 50µl (50:50 PBS:Matrigel) were transplanted subcutaneously into the mammary fat pads of balb/c nude mice and 50 days later the tumour was excised from the sacrificed mouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tumor tissues were collected in Allprotect tissue reagent kit and then processed using the Rneasy Microarray Tissue Mini Kit according to manufacturer’s protocol (tissues were lysed mechanically using the Tissue Lyser II).
Libraries were constructed with theTruSeq mRNA Paired-End kit per manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days. .
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: B249
ABX_4
|
| Data processing |
Reads were cleaned with trimmomatic (v0.36) and tagdust (v2.33) .
Reads were separately mapped to the human (Hg38) and mouse (mm10) genomes (HISAT2 v2.04). Only concordantly mapped reads were kept, and reads that mapped to both genomes were discarded (Picard)
Gene counts were obtained using Stringtie and Ballgown
TMM and library size normalized in EdgeR
Genome_build: Hg38 and mm10
Supplementary_files_format_and_content: normalised counts for Human and Mouse reads.
|
| |
|
| Submission date |
Oct 11, 2018 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Kristine Hardy |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Canberra
|
| Lab |
Cytokine Gene Expression
|
| Street address |
University of Canberra
|
| City |
Bruce |
| State/province |
ACT |
| ZIP/Postal code |
0200 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE121119 |
Using a xenograft model and RNA-seq to differentiate between the tumour and tumour microenvironment transcriptome |
|
| Relations |
| BioSample |
SAMN10231506 |
| SRA |
SRX4862500 |
